Hi, all,
I used pdb4amber to convert some pdb files, and I found there maybe some problems of pdb4amber in converting pdb files.
The original pdb file is 1NB5, which have some insertion residues. For example, there is a residue numberd as "10A" in the following segment:
(Acording to
http://www.wwpdb.org/documentation/format33/sect9.html#ATOM, column 27 is "Code for insertion of residues". And, "Alphabet letters are commonly used for insertion code. The insertion code is used when two residues have the same numbering. The combination of residue numbering and insertion code defines the unique residue.")
ATOM 83 N LYS A 10 30.107 -15.634 23.138 1.00 67.08 N
ATOM 84 CA LYS A 10 28.941 -15.747 24.014 1.00 56.56 C
ATOM 85 C LYS A 10 27.928 -16.733 23.455 1.00 61.37 C
ATOM 86 O LYS A 10 27.328 -17.517 24.192 1.00 62.22 O
ATOM 87 CB LYS A 10 28.270 -14.383 24.191 1.00 54.77 C
ATOM 88 CG LYS A 10 29.093 -13.376 24.965 1.00 55.52 C
ATOM 89 CD LYS A 10 28.238 -12.645 25.979 0.00 61.74 C
ATOM 90 CE LYS A 10 29.044 -12.324 27.226 0.00 65.26 C
ATOM 91 NZ LYS A 10 28.449 -11.179 27.972 0.00 55.65 N
ATOM 92 N GLY A 10A 27.739 -16.676 22.143 1.00 62.44 N
ATOM 93 CA GLY A 10A 26.810 -17.569 21.489 1.00 65.12 C
ATOM 94 C GLY A 10A 26.878 -17.423 19.979 1.00 65.60 C
ATOM 95 O GLY A 10A 27.953 -17.302 19.387 1.00 71.81 O
ATOM 96 N ASN A 11 25.713 -17.477 19.351 1.00 66.31 N
ATOM 97 CA ASN A 11 25.587 -17.341 17.907 1.00 55.56 C
ATOM 98 C ASN A 11 25.044 -15.927 17.772 1.00 48.85 C
ATOM 99 O ASN A 11 23.845 -15.717 17.594 1.00 65.33 O
After convertion of pdb4amber, the segment is follows, in which the "10A" residue is written as residue "11" and "12". It was messed up!
ATOM 83 N LYS A 10 30.107 -15.634 23.138 1.00 67.08 N
ATOM 84 CA LYS A 10 28.941 -15.747 24.014 1.00 56.56 C
ATOM 85 C LYS A 10 27.928 -16.733 23.455 1.00 61.37 C
ATOM 86 O LYS A 10 27.328 -17.517 24.192 1.00 62.22 O
ATOM 87 CB LYS A 10 28.270 -14.383 24.191 1.00 54.77 C
ATOM 88 CG LYS A 10 29.093 -13.376 24.965 1.00 55.52 C
ATOM 89 CD LYS A 10 28.238 -12.645 25.979 0.00 61.74 C
ATOM 90 CE LYS A 10 29.044 -12.324 27.226 0.00 65.26 C
ATOM 91 NZ LYS A 10 28.449 -11.179 27.972 0.00 55.65 N
ATOM 92 N GLY A 11 27.739 -16.676 22.143 1.00 62.44 N
ATOM 93 CA GLY A 12 26.810 -17.569 21.489 1.00 65.12 C
ATOM 94 C GLY A 12 26.878 -17.423 19.979 1.00 65.60 C
ATOM 95 O GLY A 12 27.953 -17.302 19.387 1.00 71.81 O
ATOM 96 N ASN A 13 25.713 -17.477 19.351 1.00 66.31 N
ATOM 97 CA ASN A 13 25.587 -17.341 17.907 1.00 55.56 C
ATOM 98 C ASN A 13 25.044 -15.927 17.772 1.00 48.85 C
ATOM 99 O ASN A 13 23.845 -15.717 17.594 1.00 65.33 O
I also tried to convert pdb files by convert.pl of MMTSB tools (www.mmtsb.org).
And its convertion result is follow, in which the residue "10A" was thrown away.
As as result, the chain was broken!
ATOM 83 N LYS A 10 30.107 -15.634 23.138 1.00 67.08 P01A
ATOM 84 CA LYS A 10 28.941 -15.747 24.014 1.00 56.56 P01A
ATOM 85 C LYS A 10 27.928 -16.733 23.455 1.00 61.37 P01A
ATOM 86 O LYS A 10 27.328 -17.517 24.192 1.00 62.22 P01A
ATOM 87 CB LYS A 10 28.270 -14.383 24.191 1.00 54.77 P01A
ATOM 88 CG LYS A 10 29.093 -13.376 24.965 1.00 55.52 P01A
ATOM 89 CD LYS A 10 28.238 -12.645 25.979 0.00 61.74 P01A
ATOM 90 CE LYS A 10 29.044 -12.324 27.226 0.00 65.26 P01A
ATOM 91 NZ LYS A 10 28.449 -11.179 27.972 0.00 55.65 P01A
ATOM 96 N ASN A 11 25.713 -17.477 19.351 1.00 66.31 P01A
ATOM 97 CA ASN A 11 25.587 -17.341 17.907 1.00 55.56 P01A
ATOM 98 C ASN A 11 25.044 -15.927 17.772 1.00 48.85 P01A
ATOM 99 O ASN A 11 23.845 -15.717 17.594 1.00 65.33 P01A
So, it seems that the pdb file preparation is not a easy task. Could any one tell me a better method to convert such pdb files?
Best,
Anbang
------------------
Physics Department, Central China Normal University, China
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Received on Sun Nov 09 2014 - 19:00:02 PST
